Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.

Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in alternative splicing regulation. Therefore, we wanted to test whether PKC activation in diabetic hearts induces alternative splicing abnormalities. Here, using RNA sequencing we identified a set of 22 alternative splicing events that undergo a developmental switch in splicing, and we confirmed that splicing reverts to an embryonic pattern in adult diabetic hearts. This network of genes has important functions in RNA metabolism and in developmental processes such as differentiation. Importantly, PKC isozymes α/ß control alternative splicing of these genes via phosphorylation and up-regulation of the RNA-binding proteins CELF1 and Rbfox2. Using a mutant of CELF1, we show that phosphorylation of CELF1 by PKC is necessary for regulation of splicing events altered in diabetes. In summary, our studies indicate that activation of PKCα/ß in diabetic hearts contributes to the genome-wide splicing changes through phosphorylation and up-regulation of CELF1/Rbfox2 proteins. These findings provide a basis for PKC-mediated cardiac pathogenesis under diabetic conditions.

Integrating input output analysis with risk assessment to evaluate the population risk of arsenic.

Multimedia and site-specific risk assessments (RA) of major sources releasing arsenic (As) were converted into sector-based risk coefficients, which were integrated with the Input Output Table (IO) to analyze the association between sector activities and health risks. The developed IO-RA framework is a valuable tool for unfolding the risk chain linking the receptors, exposure pathways, emission sources, and production and consumption activities associated with various industrial sectors. The enlarged decision space along the chain can then be considered in planning risk management strategies. This case study estimates that air emissions of As result in 1.54 carcinogenic cases. Export is the primary driving force and accounts for approximately 48% of the final demand that leads to population risks of As. The ranking of the contribution of the five sectors in terms of total population risks is as follows: electricity supply (1.06E+00), steelmaking (2.2 × 10(-1)), cement kilns (1.50 × 10(-1)), semiconductor manufacturing (6.34 × 10(-2)) and incinerators (4.31 × 10(-2)). The electricity supply, steelmaking industry, and cement kilns are the major sectors, not only because their emissions directly cause risk but also because they have a stronger influence on the risk generated by other sectors.

Arginine methylation of REF/ALY promotes efficient handover of mRNA to TAP/NXF1.

The REF/ALY mRNA export adaptor binds TAP/NXF1 via an arginine-rich region, which overlaps with its RNA-binding domain. When TAP binds a REF:RNA complex, it triggers transfer of the RNA from REF to TAP. Here, we have examined the effects of arginine methylation on the activities of the REF protein in mRNA export. We have mapped the arginine methylation sites of REF using mass spectrometry and find that several arginines within the TAP and RNA binding domains are methylated in vivo. However, arginine methylation has no effect on the REF:TAP interaction. Instead, arginine methylation reduces the RNA-binding activity of REF in vitro and in vivo. The reduced RNA-binding activity of REF in its methylated state is essential for efficient displacement of RNA from REF by TAP in vivo. Therefore, arginine methylation fine-tunes the RNA-binding activity of REF such that the RNA-protein interaction can be readily disrupted by export factors further down the pathway.

Mutually exclusive interactions drive handover of mRNA from export adaptors to TAP.

Adaptor proteins stimulate the nuclear export of mRNA, but their mechanism of action remains unclear. Here, we show that REF/ALY binds mRNA; but upon formation of a ternary complex with TAP the RNA is transferred from REF to TAP, and overexpression of TAP displaces REF from mRNA in vivo. RNA is also handed over from two other adaptors, 9G8 and SRp20 to TAP upon formation of a ternary complex. Interestingly, the RNA-binding affinity of TAP is enhanced 4-fold in vitro once it is complexed with REF. 9G8 and SRp20 also enhance the TAP RNA-binding activity in vitro. Consistent with a model in which TAP directly binds mRNA handed over from adaptors during export, we show that TAP binds mRNA in vivo by an arginine-rich motif in its N-terminal domain. The importance of direct TAP-mRNA interactions is confirmed by the observation that a mutant form of TAP that fails to bind mRNA but retains the ability to bind REF does not function in mRNA export.

Applying multi-criteria decision-making to improve the waste reduction policy in Taiwan.

Over the past two decades, the waste reduction problem has been a major issue in environmental protection. Both recycling and waste reduction policies have become increasingly important. As the complexity of decision-making has increased, it has become evident that more factors must be considered in the development and implementation of policies aimed at resource recycling and waste reduction. There are many studies focused on waste management excluding waste reduction. This study paid more attention to waste reduction. Social, economic, and management aspects of waste treatment policies were considered in this study. Further, a life-cycle assessment model was applied as an evaluation system for the environmental aspect. Results of both quantitative and qualitative analyses on the social, economic, and management aspects were integrated via the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) method into the comprehensive decision-making support system of multi-criteria decision-making (MCDM). A case study evaluating the waste reduction policy in Taoyuan County is presented to demonstrate the feasibility of this model. In the case study, reinforcement of MSW sorting was shown to be the best practice. The model in this study can be applied to other cities faced with the waste reduction problems.

A systemic health risk assessment for the chromium cycle in Taiwan.

Health risk assessment (HRA) has been recognized as a useful tool for identifying health risks of human activities. In particular, this method has been well applied to spatially defined units, such as a production plant, a treatment facility, and a contaminated site. However, the management strategies based on the risk information will be more efficient if the comprehensive picture of total risks from all kinds of sources is depicted. In principle, the total risks can be obtained when all risk sources are assessed individually. Apparently, this approach demands huge amount of efforts. This study develops a methodology that combines substance flow and risk estimation to facilitate examination of risk in a systemic way and provide comprehensive understanding of risk generation and distribution corresponding to flows of substances in the anthroposphere and the environment. Substance flow analysis (SFA) and HRA method is integrated to produce a systemic risk assessment method, from which substance management schemes can be derived. In this study, the chromium cycle in Taiwan is used as an example to demonstrate the method, by which the associated substance flow in the economy and the risk caused by the substance in the environmental system is determined. The concentrations of pollutants in the environmental media, the resultant risks and hazard quotients are calculated with the widely-used CalTOX multimedia model.

A novel sustainable decision making model for municipal solid waste management.

This paper reviews several models developed to support decision making in municipal solid waste management (MSWM). The concepts underlying sustainable MSWM models can be divided into two categories: one incorporates social factors into decision making methods, and the other includes public participation in the decision-making process. The public is only apprised or takes part in discussion, and has little effect on decision making in most research efforts. Few studies have considered public participation in the decision-making process, and the methods have sought to strike a compromise between concerned criteria, not between stakeholders. However, the source of the conflict arises from the stakeholders' complex web of value. Such conflict affects the feasibility of implementing any decision. The purpose of this study is to develop a sustainable decision making model for MSWM to overcome these shortcomings. The proposed model combines multicriteria decision making (MCDM) and a consensus analysis model (CAM). The CAM is built up to aid in decision-making when MCDM methods are utilized and, subsequently, a novel sustainable decision making model for MSWM is developed. The main feature of CAM is the assessment of the degree of consensus between stakeholders for particular alternatives. A case study for food waste management in Taiwan is presented to demonstrate the practicality of this model.

dsRBM1 and a proline-rich domain of RNA helicase A can form a composite binder to recognize a specific dsDNA.

The double-stranded RNA-binding motif (dsRBM) is a widely distributed motif frequently found within proteins with sequence non-specific RNA duplex-binding activity. In addition to the binding of double-stranded RNA, some dsRBMs also participate in complex formation via protein-protein interactions. Interestingly, a lot of proteins containing multiple dsRBMs have only some of their dsRBMs with the expected RNA duplex-binding competency proven, while the functions of the other dsRBMs remain unknown. We show here that the dsRBM1 of RNA helicase A (RHA) can cooperate with a C-terminal domain of proline-rich content to gain novel nucleic acid-binding activities. This integrated nucleic acid-binding module is capable of associating with the consensus sequences of the constitutive transport element (CTE) RNA of type D retrovirus against RNA duplex competitors. Remarkably, binding activity for double-stranded DNA corresponding to the consensus sequences of the cyclic-AMP responsive element also resides within this composite nucleic acid binder. It thus suggests that the dsRBM fold can be used as a platform for the building of a ligand binding module capable of non-RNA macromolecule binding with an accessory sequence, and functional assessment for a newly identified protein containing dsRBM fold should be more cautious.

Analysis of arginine and lysine methylation utilizing peptide separations at neutral pH and electron transfer dissociation mass spectrometry.

Arginine and lysine methylation are widespread protein post-translational modifications. Peptides containing these modifications are difficult to retain using traditional reversed-phase liquid chromatography because they are intrinsically basic/hydrophilic and often fragment poorly during collision induced fragmentation (CID). Therefore, they are difficult to analyze using standard proteomic workflows. To overcome these caveats, we performed peptide separations at neutral pH, resulting in increased retention of the hydrophilic/basic methylated peptides before identification using MS/MS. Alternatively trifluoroacetic acid (TFA) was used for increased trapping of methylated peptides. Electron-transfer dissociation (ETD) mass spectrometry was then used to identify and characterize methylated residues. In contrast to previous reports utilizing ETD for arginine methylation, we observed significant amount of side-chain fragmentation. Using heavy methyl stable isotope labeling with amino acids in cell culture it was shown that, similar to CID, a loss of monomethylamine or dimethylamine from the arginine methylated side-chain during ETD can be used as a diagnostic to determine the type of arginine methylation. CID of lysine methylated peptides does not lead to significant neutral losses, but ETD is still beneficial because of the high charge states of such peptides. The developed LC MS/MS methods were successfully applied to tryptic digests of a number of methylated proteins, including splicing factor proline-glutamine-rich protein (SFPQ), RNA and export factor-binding protein 2 (REF2-I) and Sul7D, demonstrating significant advantages over traditional LC MS/MS approaches.

The Health Risk assessment of Pb and Cr leached from fly ash monolith landfill.

As of 2004, nearly two hundred thousand tons of fly ash monoliths are created each year in Taiwan to confine heavy metals for reducing the leaching quantity by precipitation. However, due to abnormal monolith fracture, poorly liner quality or exceeding usage over designed landfill capacity, serious groundwater pollution of the landfills has been reported. This research focuses on Pb and Cr leaching from monolithic landfill to assess the risk of groundwater pollution in the vicinity. The methodology combines water budget simulations using HELP model with fate and risk simulations using MMSOILS model for 5 kinds of landfill structures and 2 types of leaching models, and calculates the risk distribution over 400 grids in the down gradient direction of groundwater. The results demonstrated that the worst liner quality will cause the largest risk and the most significant exposure pathway is groundwater intake, which accounted for 98% of the total risk. Comparing Pb and Cr concentrations in the groundwater with the drinking water standards, only 14.25% of the total grids are found to be under 0.05 mg/L of Pb, and over 96.5% of the total grids are in the safety range of Cr. It indicates that Pb leaching from fly ash monolithic landfills may cause serious health risks. Without consideration of the parameters uncertainty, the cancer and noncancer risk of Pb with the sanitary landfill method was 4.23E-07 and 0.63, respectively, both under acceptable levels. However, by considering the parameters uncertainty, the non-carcinogenic risk of Pb became 1.43, exceeding the acceptable level. Only under the sealed landfill method was the hazard quotient below 1. It is important to use at least the sealed landfill for fly ash monoliths containing lead to effectively reduce health risks.

UIF, a New mRNA export adaptor that works together with REF/ALY, requires FACT for recruitment to mRNA.

Messenger RNA (mRNA) export adaptors play an important role in the transport of mRNA from the nucleus to the cytoplasm. They couple early mRNA processing events such as 5' capping and 3' end formation with loading of the TAP/NXF1 export receptor onto mRNA. The canonical adaptor REF/ALY/Yra1 is recruited to mRNA via UAP56 and subsequently delivers the mRNA to NXF1 [1]. Knockdown of UAP56 [2, 3] and NXF1 [4-7] in higher eukaryotes efficiently blocks mRNA export, whereas knockdown of REF only causes a modest reduction, suggesting the existence of additional adaptors [8-10]. Here we identify a new UAP56-interacting factor, UIF, which functions as an export adaptor, binding NXF1 and delivering mRNA to the nuclear pore. REF and UIF are simultaneously found on the same mRNA molecules, and both proteins are required for efficient export of mRNA. We show that the histone chaperone FACT specifically binds UIF, but not REF, via the SSRP1 subunit, and this interaction is required for recruitment of UIF to mRNA. Together the results indicate that REF and UIF represent key human adaptors for the export of cellular mRNAs via the UAP56-NXF1 pathway.

Structural and functional analysis of RNA and TAP binding to SF2/ASF.

The serine/arginine-rich (SR) protein splicing factor 2/alternative splicing factor (SF2/ASF) has a role in splicing, stability, export and translation of messenger RNA. Here, we present the structure of the RNA recognition motif (RRM) 2 from SF2/ASF, which has an RRM fold with a considerably extended loop 5 region, containing a two-stranded beta-sheet. The loop 5 extension places the previously identified SR protein kinase 1 docking sequence largely within the RRM fold. We show that RRM2 binds to RNA in a new way, by using a tryptophan within a conserved SWQLKD motif that resides on helix alpha1, together with amino acids from strand beta2 and a histidine on loop 5. The linker connecting RRM1 and RRM2 contains arginine residues, which provide a binding site for the mRNA export factor TAP, and when TAP binds to this region it displaces RNA bound to RRM2.